EIF2B3 (Eukaryotic Translation Initiation Factor 2B Subunit Gamma)

2021-01-01   Gözde Köksal-Biçakci , Didem Naz Dioken , Ayse Elif Erson-Bensan 

Department of Biological Sciences, Middle East Technical University, Ankara, TURKEY, gozdek@metu.edu.tr; didem.doken@metu.edu.tr; erson@metu.edu.tr

Identity

LOCATION
1p34.1
IMAGE
Atlas Image
LEGEND
Local order of EIF2B3 is shown on chromosome 1. The direction of arrows indicates transcriptional direction on the chromosome and arrow sizes indicate the approximate gene sizes.
LOCUSID
ALIAS
Eukaryotic Translation Initiation Factor 2B, Subunit 3 Gamma, 58kDa, Translation Initiation Factor EIF-2B Subunit Gamma, EIF-2B GDP-GTP Exchange Factor Subunit Gamma, Eukaryotic Translation Initiation Factor 2B, Subunit 3 (Gamma, 58kD), EIF2Bgamma, eIF2B&gamma,.
FUSION GENES

Abstract

Eukaryotic Translation Initiation Factor 2B Subunit Gamma (EIF2B3) gene maps to 1p34.1, consists of 12 exons and 11 introns (NCBI Reference Sequence: NC_000001.11: 44850522-44986722). The locus generates three transcripts as a result of alternative splicing. EIF2B3 protein is composed of 452 amino acids and it is one of the important subunits of EIF2B decameric complex with guanine nucleotide exchange factor (GEF) activity. EIF2B3 protein plays a crucial role in the rate-limiting step of translation initiation.

DNA/RNA

Note

EIF2B3 gene consists of 12 exons and 11 introns. The gene maps to 1p34.1 and is 136,201 bp long (NCBI Reference Sequence: NC_000001.11: 44850522-44986722). Highlighted in orange is the protein coding sequence from exons 2-12 (Figure 2).
Atlas Image
EIF2B3 gene has 12 exons and 11 introns. Numbers above indicate the exons. Orange boxes represent the exons/protein-coding regions while grey boxes represent the exons/untranslated regions.

Description

EIF2B3 gene is 136,201 bp long and is on the minus strand. This gene has 12 exons.

Transcription

EIF2B3 produces 3 coding mRNA transcripts (1900 bp, 1607 bp, and 1923 bp). The first transcript variant is the longest one with 12 exons. The difference between the first and the third variant is the absence of the 11th exon in the third variant resulting in a shorter transcript. The second variant lacks the last two coding exons of the first variant and is the shortest transcript variant among the three isoforms (NCBI, 2020).

Proteins

Note

The gene coding EIF2B3 encodes a 452 amino acid protein. This protein is a member of the subunits of initiation factor eIF2B. It has an estimated molecular weight of 50,240 kDa (Wortham et al., 2014).
Atlas Image
EIF2B3 has two functional domains; one nucleotidyl transferase domain (NT) and one acyl transferase (AT) domain. The numbers below the boxes indicate the amino acid numbers.

Description

EIF2B3 protein catalyzes the exchange of GDP for GTP bound to the eukaryotic initiation factor 2. Through its highly conserved NT domain, EIF2B3 is an essential component of a decameric complex with other EIF2B subunits required for translational initiation and regulation (Pavitt, 2005). Additionally, AT domain containing hexad repeats of isoleucyl residues (also termed as I-patch region) plays a key role in the interaction of the catalytic subcomplex of the EIF2B complex with other domains (Wang et al., 2012).

Expression

EIF2B3 protein is detected in almost all human tissues. The expression is mostly cytoplasmic in human tissues (The Human Protein Atlas, 2020). The protein expression for EIF2B3 is highest in pancreas, thyroid gland, and breast tissue (Samaras et al., 2019)

Localisation

EIF2B3 protein localizes to the cytosol with the other proteins of the EIF2B complex (Hodgson et al., 2019).

Function

EIF2B3, is one of the important subunits of the decameric complex of EIF2B with guanine nucleotide exchange factor (GEF) activity. During the initiation of translation, eukaryotic initiation factor-2, a heterotrimeric GTPase, forms a ternary complex with Met-tRNAi which is delivered to 40S ribosomal subunit (Pavitt, 2005). After the recognition of AUG codon by Met-tRNAi at the P site, eIF2-GTP is hydrolyzed resulting in the release of inactive eIF2-GDP, which aids 40S and 60S ribosomal subunit assembly (Pavitt, 2005). In this inactive state of eIF2, the initiation of new rounds of translation is not possible unless there is a switch from GTP to GDP (Mohammad-Qureshi, Jennings, & Pavitt, 2008). Hence, eIF2B activating the eIF2 by exchanging GDP for GTP with its GEF activity is a key factor for translation (Mohammad-Qureshi et al., 2008).
EIF2B has five subunits (α - ε), which form the regulatory and the catalytic sub-complexes. EIF2Bγ (EIF2B3) together with EIF2B5 (EIF2Bε) form the catalytic sub-complexes (EIF2Bcat), while EIF2B1 (EIF2Bα), EIF2B2 (EIF2Bβ), and EIF2B4 (EIF2Bδ) subunits form the regulatory sub-complexes (EIF2Breg) (Hinnebusch & Yang, 1996; Kashiwagi et al., 2016). The catalytic sub-complex is responsible for the GEF activity of the complex. Some studies suggest that eIF2Bε itself is enough for GEF activity in vitro; however, activity may be very low without EIF2B3 (Gomez, Mohammad, & Pavitt, 2002). On the contrary, another study suggests that γ and ε subunits together have the GEF function; indeed, the pyrophosphorylase-like (PL) domain of γ subunit is the main responsible part for GTP binding (Gordiyenko et al., 2014).
EIF2B3 was reported to be a cofactor for hepatitis C virus (HCV) IRES-mediated protein translation (Kruger et al., 2000).
The expression level, availability and activity eukaryotic initiation factors are usually regulated by key signaling pathways, such as phosphatidylinositol 3-kinase (PI3K)/AKT, mitogen-activated protein kinase (MAPK), and mammalian target of rapamycin (mTOR) pathways. Deregulation of these pathways may have significant effect on translation initiation through initiation factors (Hao et al., 2020).

Homology

EIF2B3 gene has high homology across species, including chimpanzee, Rhesus monkey, dog, cow, mouse, rat, chicken, zebrafish, fruit fly, mosquito, C.elegans, S.pombe, M.oryzae, N.crassa, A.thaliana, rice, and frog (NCBI HomoloGene, 2020). So far, 317 orthologous genes to human EIF2B3 gene have been reported (NCBI, 2020).

Mutations

Note

According to COSMIC database, 683 samples out of 37,420 unique samples from cancer patients have EIF2B3 mutations. There are 143 unique substitution mutations in 860 cancer patients for EIF2B3 gene. 14% of all the reported mutations are missense mutations (COSMIC database, 2018). Mutation burden is generally low for different cancer types, but the alteration frequency is the highest for endometrial carcinoma with 5.12% in 586 cases (cBioPortal database) (Cerami et al., 2012; Gao et al., 2013).
EIF2B3 mutations may also be related to vanishing white matter disease and ovarian failure (La Piana et al., 2012).

Implicated in

Top note
EIF2B3 has been implicated in leukoencephalopathies.
Entity name
Vanishing White Matter disease (VWM)/ Childhood Ataxia with Diffuse Central Nervous System Hypomyelinization (CACH)
Disease
One of the most common leukoencephalopathies in children is the vanishing white matter (VWM) disease/childhood ataxia with diffuse central nervous system hypomyelination. This autosomal recessive disease is mostly common in early childhood, but it also affects adults (Zhang et al., 2015). Mutation in any of the five genes encoding the subunits of the eukaryotic translation initiation factor 2B (EIF2B), including EIF2B3, is known to be the major cause of the disease (Leegwater et al., 2001). A mutation screening on 11 Chinese patients showed that 20% of the total number of mutations found in all subunits of EIF2B mainly belongs to EIF2B3 (Wu et al., 2009). These mutations impair the EIF2B function, hence protein synthesis. Eventually, this brings the abnormalities in cerebral white matter such as demyelination of white matter, which is replaced by the cerebrospinal fluid (Fogli & Boespflug-Tanguy, 2006). Neurological deteriorations and even death may occur because of the vanishing of the white matter. Additionally, in the cases of adult-onset disease, women may experience leukoencephalopathy together with ovarian failure, which is described as ovarioleukodystrophy (Fogli et al., 2003)
Prognosis
A long term follow-up study on Chinese children with VWM showed that the median survival time for patients is 8.83 ± 1.51 years (Zhang et al., 2015).
Entity name
Premature Ovarian Failure (POF)
Disease
eIF2B mutations, described in patients with POF with white matter abnormalities, are an uncommon cause of pure spontaneous premature ovarian failure (Fogli et al., 2004).
Entity name
Breast Cancer
Disease
PI3K/Akt/GSK-3β/ROS/eIF2B pathway might promote the growth and metastasis of breast cancer through the suppression of NK cell cytotoxicity and tumor cell susceptibility (Jin et al., 2019). The PI3K/Akt pathway inactivates GSK3B by phosphorylation at Ser9 resulting in increased ROS (reactive oxygen species). As a result of this, EIF2B phosphorylation at Ser535 is attenuated, that causes the downregulation of NKG2D (natural killer group 2 member D, a.k.a. KLRK1, killer cell lectin like receptor K1) and NKG2DL (NKG2D ligand) resulting in suppression of NK cell activity. Through this mechanism, both growth and metastasis of breast cancer is promoted in mouse (Jin et al., 2019).
Entity name
Endometrial Carcinoma
Disease
5.12% of samples obtained from 586 endometrial carcinoma patients have mutations in EIF2B3 gene (cBioPortal database) (Cerami et al., 2012; Gao et al., 2013).
Entity name
Ovarian Epithelial Tumor
Disease
In addition to the mutations, the highest amplification frequency in EIF2B3 is reported in ovarian tumors in pan-cancer studies: 4.62% for 584 cases according to cBioPortal database. (Cerami et al., 2012; Gao et al., 2013).

Bibliography

Reference NumberPubmed IDLast YearTitleAuthors
1146957592004Primary gastric lymphoma.Al-Akwaa AM et al
2261853722015Helicobacter pylori-negative gastric mucosa-associated lymphoid tissue lymphomas: A review.Asano N et al
3152136172004The role of surgery in primary gastric lymphoma: results of a controlled clinical trial.Avilés A et al
4169508582007Mucosa-associated lymphoid tissue (MALT) lymphoma: a practical guide for pathologists.Bacon CM et al
5108164062000Low grade gastric MALT Lymphoma: radiographic findings.Brown JA et al
619367851991Primary B-cell gastric lymphoma: a clinicopathological study of 145 patients.Cogliatti SB et al
7173376462007Infectious agents as causes of non-Hodgkin lymphoma.Engels EA et al
8271026582016The Toronto Consensus for the Treatment of Helicobacter pylori Infection in Adults.Fallone CA et al
9171564032007Primary gastric lymphoma pathogenesis and treatment: what has changed over the past 10 years?Ferrucci PF et al
10187941812008Treatment of Helicobacter pylori infection.Fuccio L et al
1173887631980Gastrointestinal involvement in non-Hodgkin's lymphoma.Herrmann R et al
1286084741996Early gastric lymphoma: a clinicopathologic study of ten patients, literature review, and comparison with early gastric adenocarcinoma.Kitamura K et al
1319255051991Pathology and clinical features of gastro-intestinal lymphoma in Saudi Arabia.Kyriacou C et al
14147243032004Immunoproliferative small intestinal disease associated with Campylobacter jejuni.Lecuit M et al
15175464742007Prognostic factors in primary gastric lymphoma.Medina-Franco H et al
1681457811994Helicobacter pylori infection and gastric lymphoma.Parsonnet J et al
1779523911994Primary gastric lymphomas: a clinicopathologic study with literature review.Roukos DH et al
1866272151983Primary gastric lymphoma. An analysis with emphasis on prognostic factors and radiation therapy.Shimm DS et al
19191937052009Long-term outcome following Helicobacter pylori eradication in a retrospective study of 105 patients with localized gastric marginal zone B-cell lymphoma of MALT type.Stathis A et al
2089445651996Primary non-Hodgkin lymphoma of the stomach: endoscopic pattern and prognosis in low versus high grade malignancy in relation to the MALT concept.Taal BG et al
2117759391991Primary non-Hodgkin's lymphoma of the stomach: endoscopic diagnosis and the role of surgery.Taal BG et al
22251906962014Non-Hodgkin's lymphomas, version 4.2014.Zelenetz AD et al

Citation

Gözde Köksal-Biçakci ; Didem Naz Dioken ; Ayse Elif Erson-Bensan

EIF2B3 (Eukaryotic Translation Initiation Factor 2B Subunit Gamma)

Atlas Genet Cytogenet Oncol Haematol. 2021-01-01

Online version: http://atlasgeneticsoncology.org/gene/62775/eif2b3